2017/02/07

Nature Structural & Molecular Biology Contents: 2017 Volume #24 pp 97 - 194

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TABLE OF CONTENTS

February 2017 Volume 24, Issue 2

News and Views
Articles
Corrigendum
Errata
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News and Views

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Mechanisms for targeted, purposeful mutation revealed in an APOBEC-DNA complex   pp97 - 98
Emily K Schutsky, Zachary M Hostetler and Rahul M Kohli
doi:10.1038/nsmb.3373
Targeted deamination of cytosine bases in DNA by AID/APOBEC-family enzymes is critical for proper immune function, but it also poses risks to genomic integrity. New structures reported by Harris, Aihara and colleagues offer the first glimpses into the enzyme-DNA complex and reveal both expected and unexpected insights into the DNA-binding mode involved in targeting purposeful mutation.

See also: Article by Shi et al.

Articles

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates   pp99 - 107
Michael H Hauer, Andrew Seeber, Vijender Singh, Raphael Thierry, Ragna Sack et al.
doi:10.1038/nsmb.3347
A combination of SILAC-MS, genome-wide nucleosome mapping and live-cell imaging reveal rapid histone degradation and global chromatin decompaction after the induction of DNA double-strand breaks in S. cerevisiae.

Crystal structures of human glycine receptor α3 bound to a novel class of analgesic potentiators   pp108 - 113
Xin Huang, Paul L Shaffer, Shawn Ayube, Howard Bregman, Hao Chen et al.
doi:10.1038/nsmb.3329
The structure of GlyRα3 in complex with a selective potentiator that decreases neuropathic pain in an animal model identifies a novel allosteric regulatory mechanism.

Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2)   pp114 - 122
Mariana Grieben, Ashley C W Pike, Chitra A Shintre, Elisa Venturi, Sam El-Ajouz et al.
doi:10.1038/nsmb.3343
The cryo-EM structure of human polycystin-2 (PC2) in a closed conformation reveals a domain located above the pore filter, forming an upper vestibule and making contacts with the pore and voltage-sensor-like domains.

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Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2   pp123 - 130
Martin Wilkes, M Gregor Madej, Lydia Kreuter, Daniel Rhinow, Veronika Heinz et al.
doi:10.1038/nsmb.3357
Cryo-EM structures of full-length human PC2 reveal two distinct channel states: an open conformation and a blocked conformation with Ca2+ bound at the entrance of the selectivity filter.

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B   pp131 - 139
Ke Shi, Michael A Carpenter, Surajit Banerjee, Nadine M Shaban, Kayo Kurahashi et al.
doi:10.1038/nsmb.3344
Crystal structures of human APOBEC3A and a chimera of APOBEC3B and APOBEC3A bound to ssDNA reveal an unanticipated /`U-shaped/' binding mode and provide insight into target selectivity.

See also: News and Views by Schutsky et al.

Self-correcting mismatches during high-fidelity DNA replication   pp140 - 143
Rafael Fernandez-Leiro, Julian Conrad, Ji-Chun Yang, Stefan M V Freund, Sjors H W Scheres et al.
doi:10.1038/nsmb.3348
Cryo-EM and NMR analyses of the E. coli replisome show how DNA-end fraying after mismatch incorporation at the polymerase active site enables substrate ends to reach the /`proofreading/' exonuclease site for mismatch removal.

Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex   pp144 - 151
Felix Alexander Weyer, Andrea Gumiero, Genis Valentin Gesé, Karine Lapouge and Irmgard Sinning
doi:10.1038/nsmb.3349
The yeast ribosome-associated complex (RAC) is formed by Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1. Structural analyses show Ssz1 in a hybrid conformation between the open and closed state and its substrate-binding domain completed by Zuo1.

Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex   pp152 - 161
Franziska Theresia Edelmann, Andreas Schlundt, Roland Gerhard Heym, Andreas Jenner, Annika Niedner-Boblenz et al.
doi:10.1038/nsmb.3351
Crystal structures of a localization element of ASH1 mRNA alone, in complex with its nuclear shuttling protein She2p, and in the cytoplasmic complex with She2p and She3p reveal a step-wise maturation pathway.

Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes   pp162 - 170
Joseph S Osmundson, Jayashree Kumar, Rani Yeung and Duncan J Smith
doi:10.1038/nsmb.3342
Genome-wide analyses of S. cerevisiae replisome mobility reveal overlapping roles of Pif1 and Rrm3 helicases in alleviating replication-fork arrest at tRNA genes.

Crystal structure of the MOP flippase MurJ in an inward-facing conformation   pp171 - 176
Alvin C Y Kuk, Ellene H Mashalidis and Seok-Yong Lee
doi:10.1038/nsmb.3346
The crystal structure of MurJ, a bacterial lipid II flippase involved in peptidoglycan biosynthesis and a member of the MOP transporter superfamily, reveals an inward-facing conformation and points to an alternating-access mechanism.

Structural insights into the secretin translocation channel in the type II secretion system   pp177 - 183
Zhaofeng Yan, Meng Yin, Dandan Xu, Yongqun Zhu and Xueming Li
doi:10.1038/nsmb.3350
Cryo-EM structures of secretin GspD in type II secretion systems from Escherichia coli and Vibrio cholera reveal a pentadecameric architecture, with three rings in the periplasm and β-strand-enriched gates on the outer membrane.

Structure of the immature Zika virus at 9 Å resolution   pp184 - 186
Vidya Mangala Prasad, Andrew S Miller, Thomas Klose, Devika Sirohi, Geeta Buda et al.
doi:10.1038/nsmb.3352
The cryo-EM structure of immature Zika virus shows partially ordered capsid proteins and reveals differences between pre-epidemic and epidemic strains at protein interfaces within the trimeric spikes.

Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I   pp187 - 193
Stefan Bibow, Yevhen Polyhach, Cedric Eichmann, Celestine N Chi, Julia Kowal et al.
doi:10.1038/nsmb.3345
HDL particles transport cholesterol and contain apolipoprotein A-I as their major protein. The solution structure of discoidal HDL particles reconstituted with a shortened apoA-I is now solved via a combination of NMR and EPR analyses.

Corrigendum

Top

Corrigendum: Exon-intron circular RNAs regulate transcription in the nucleus   p194
Zhaoyong Li, Chuan Huang, Chun Bao, Liang Chen, Mei Lin et al.
doi:10.1038/nsmb0217-194a

Errata

Top

Erratum: Selective integrin endocytosis is driven by interactions between the integrin α-chain and AP2   p194
Nicola De Franceschi, Antti Arjonen, Nadia Elkhatib, Konstantin Denessiouk, Antoni G Wrobel et al.
doi:10.1038/nsmb0217-194b

Erratum: BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin   p194
Ballachanda N Devaiah, Chanelle Case-Borden, Anne Gegonne, Chih Hao Hsu, Qingrong Chen et al.
doi:10.1038/nsmb0217-194c

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